BIDSify magnitude data and labels

[jcohenadad]

Motivation: we want to upload the data to OpenNeuro, so we need to BIDSify them.

The magnitude data are already in BIDS and are located here (internal server): https://data.neuro.polymtl.ca/datasets/whole-spine

The segmentation labels organized by @CharlesPageot are located here.

Here's a tree:

├── whole-spine_air_tissue_labels  --> body, lungs, trachea, sinuses
├── whole-spine_bone_discs_labels --> vertebrae, intervertebral discs
├── whole-spine_samseg_labels --> a bunch of labels in the brain, from SamSeg output. 
└── whole-spine_spine_labels --> spinal canal or spinal cord --> @CharlesPageot ?

They need to be organized according to BIDS, but for that we need to agree on the organization. Few thoughts:

Additional notes:

• the README.md seems inaccurate at some places.
• whole-spine_samseg_labels folder name is misleading
• We will need to merge the magnitude data (under 'root' of BIDS folder) and the segmentations (under 'derivatives/labels')
• We will need to decide how we want to combine all the segmentation files. This will depend on how @CharlesPageot 's code to process these data look like. @CharlesPageot can you please upload your code on GH asap so we can start organizing the files accordingly.

Important

The magnitude BIDS data already include some labels, that were likely generated by @NathanMolinier. I will do some digging to understand what labels already exist, and which ones are duplicates of what @CharlesPageot shared in the GDrive folder.

[jcohenadad]

OK, good news, the dataset and some of the labels are already in BIDS format. More details:

• sub-amuAL_T1w_label-brain_dseg.nii.gz --> SAMSEG labels head labels
• sub-amuAL_T1w_label-CSF_seg --> CSF
• sub-amuAL_T1w_label-SC_seg --> spinal cord
• sub-amuAL_T1w_label-spine_dseg --> discrete vertebrae + intervertebral discs (one value per level)

So, what we need to do next, is to develop code that:

• cleans up the SAMSEG labels, ie: only keep the important ones (eye, skull, fat?) @CharlesPageot your input needed here. You mentioned you did this in Slicer3D, what exactly did you do, and where did you put the corrected labels? Are the corrected labels under the GDrive folder whole-spine_samseg_labels or does this folder contain the direct (ie not manually corrected) output from SAMSEG?
• (MB) takes the labels from whole-spine_air_tissue_labels (from gdrive, lungs, trachea, sinuses) and add them to the git-annex dataset
  • https://data.neuro.polymtl.ca/datasets/whole-spine/pulls/5
• (MB) assembles all the labels into a single NIfTI file, with tissue value that are consistent with https://github.com/shimming-toolbox/tissue-to-MRproperty?tab=readme-ov-file#look-up-table
  • branch: mb/single-nifti
• add those labels to the git-annex dataset
• package and upload to OpenNeuro

[mathieuboudreau]

assembles all the labels into a single NIfTI file, with tissue value that are consistent with https://github.com/shimming-toolbox/tissue-to-MRproperty?tab=readme-ov-file#look-up-table

From a quick check, it looks like some of the air-tissue labels will overlap with the SAMSEG generated labels, eg,

Though maybe this won't be an issue after first point is done (cleans up the SAMSEG labels, ie: only keep the important ones (eye, skull, fat?)), we should make sure to write code that checks this and decide how to handle it (unless we want a 4D nifti, but my guess is no)

[mathieuboudreau]

The T1w/T2w images of the subjects have not been defaced,

https://docs.openneuro.org/user_guide.html
Uploading your dataset
4. You will need to ensure that either all structural scans have been defaced (we recommend the pydeface tool) or that you have explicit participant consent and ethical authorization to publish without defacing.

Considering that information, should deface we the T1w/T2w volumes prior to uploading to OpenNeuro?

[mathieuboudreau]

takes the labels from whole-spine_air_tissue_labels (from gdrive, lungs, trachea, sinuses) and add them to the git-annex dataset

Working on this

[mathieuboudreau]

The segmentation labels organized by @CharlesPageot are located here.

sub-unfErssm021 is missing their air-tissue labels in the GDrive, @CharlesPageot are you aware and if so, why?

[mathieuboudreau]

The segmentation labels organized by @CharlesPageot are located here.

sub-unfErssm021 is missing their air-tissue labels in the GDrive, @CharlesPageot are you aware and if so, why?

Ah - that subject only had T2w data.

There's other subjects missing labels due to the raw data, eg sub-unfErssm001 has no brain labels due to the mispositioned T1w volume. Something to consider while coding the merging/splitting of labels

[mathieuboudreau]

takes the labels from whole-spine_air_tissue_labels (from gdrive, lungs, trachea, sinuses) and add them to the git-annex dataset

Working on this

Labels added to branch mb/air-tissue-labels, PR opened (https://data.neuro.polymtl.ca/datasets/whole-spine/pulls/5), but its a WIP because I'm missing json sidecar information:

• date labels were computed
• totalseg version that was used

Who would know this, @CharlesPageot ?

[sriosq]

Hello @mathieuboudreau. Regarding the conflicting labels. With the code in tissue to MR property, we have implemented a function that checks if all the pixels have values according to the dictionary of labels used.

[mathieuboudreau]

assembles all the labels into a single NIfTI file, with tissue value that are consistent with https://github.com/shimming-toolbox/tissue-to-MRproperty?tab=readme-ov-file#look-up-table

On this now.

assembles all the labels into a single NIfTI file, with tissue value that are consistent with https://github.com/shimming-toolbox/tissue-to-MRproperty?tab=readme-ov-file#look-up-table

This instruction wasn't clear to me - at first you say to merge all the labels into one file of labels, but after say that the tissue values (in the nifti file?) should be consistent with that table.

Do you mean,

1. simply assemble all the labels into a single nifti files, such that the label values in that file are consistent with that repo's label value definition for all tissues, i.e. these dictionaries?

or

2. assemble all the labels into a single nifti file, and then using that label file generate additional nifti files for each MR property (i.e. for each subject, generate whole-body label file +
   T1, T2, T2*, PD, and Susceptibility files)?

Regardless, I can start working on it and adjust as needed

[jcohenadad]

Considering that information, should deface we the T1w/T2w volumes prior to uploading to OpenNeuro?

No, this will defeat the purpose of the project (ie: design shim coils for the head-- if part of the head is missing, then that's problematic. Let's hear back from the Marseille folks what they say.

[jcohenadad]

date labels were computed
totalseg version that was used
Who would know this, @CharlesPageot ?

Possibly @Nilser3 and/or @NathanMolinier

[jcohenadad]

simply assemble all the labels into a single nifti files, such that the label values in that file are consistent with that repo's label value definition for all tissues, i.e. these dictionaries?

yes, that's exactly what I meant, sorry for the lack of clarity